The kooky cleric accused of stalking Conan O’Brien went AWOL in Boston yesterday, sparking a frantic police search after his father warned he may be “homicidal.”

But the Rev. David Ajemian was ushered back to his parents’ home by a fellow priest hours later and said he had no idea police were looking for him.

Authorities said Ajemian was “just out and about because he was despondent.”

The troubled priest later checked himself into an area hospital for evaluation, police sources said.

It was a tense afternoon for family and authorities – and perhaps for Faye Dunaway and Paul Simon as well.

Just hours before he went missing, Ajemian told The Post that he would follow the court’s restraining order and stop badgering O’Brien, but added he’s interested in meeting the “Bonnie and Clyde” star and the superstar songsmith.

Ajemian’s father called cops at around 3:15 p.m. to report his son, who was released from jail Friday on $2,500 bail, had been missing.

“Essentially, his family is concerned because [his] doctor feels that in addition to being bipolar he could be suicidal or homicidal,” said Boston police spokesman James Kenneally.

The priest had been missing for about three hours when his father called police, he said.

Earlier in the day, the celeb-obsessed sermonizer said he had moved on from O’Brien, and was now intrigued by Dunaway and Simon.

“I really loved his music,” he said of Simon.

As for Dunaway, he claims the two met in the mid-1990s when both were studying Catholicism at St. Paul’s Parish in Cambridge, Mass.

“I wrote her agent,” he said. “I never heard anything back.”

The ’70s screen queen did convert to Catholicism at that church about 10 years ago, according to press accounts.

She could not be reached for comment to confirm meeting Ajemian.

In the nearly hour-long interview, Ajemian also confessed he regretted some of the stream of letters he sent to O’Brien.

“I never had any intention of physically harming him in any way,” he insisted.

“I do feel sad that some of the correspondence were interpreted in that way.”

But he said he didn’t feel sorry for writing in one letter that John McEnroe “assaulted me once in the seventh grade” when they were both attending a Manhattan private school.

“I was giving him a little back-talk,” said Ajemian, who attended Trinity School at the same time as the tennis great.

“He grabbed me and started throwing me around the room, ridiculing me in front of my classmates.”

Ajemian and O’Brien attended Harvard at the same time in the 1980s and lived in the same dorm, but never met.

His one and only encounter with the TV host came much later in life – at a charity event in Lawrence, Mass.

He was invited to a food-pantry fund-raiser, he said, by the O’Brien family, whom he met when he served at the family’s hometown church in Brookline, Mass.

During their brief interlude, he said, they discovered that at different times they lived in the same Central Park West building.

“He seemed interested in some of our connections,” Ajemian recalled.

But the infatuated priest was more than interested in the links. Cops said he harangued the former “Saturday Night Live” writer with letters and postcards at O’Brien’s home and his office.

Police sources said Ajemian followed O’Brien to Italy and California, but Ajemian insists that was just an “unusual coincidence.

“I went to Tuscany and visited the town of Luca purely on my own initiative,” he said.

A postcard from Italy spurred the authorities to action, sources said, and sent the investigation into overdrive.

“It was my final correspondence to say I was coming to the show,” Ajemian said.

When he turned up at Rockefeller Center on Nov. 2 for the taping, he was arrested waiting in line.

His week on Rikers Island was “a horrible experience,” and odd for him because he’d worked as a prison chaplain.

He vowed to put it all behind him, but wouldn’t mind a little shout-out from the show.

“I’d like him to perhaps acknowledge the fact that he’s aware of this drama,” he said. “For my sake.”